Genomic Analysis of Propane Metabolism in Methyl Tert-Butyl Ether-Degrading Mycobacterium Sp. Strain ENV421

Propane Monooxygenases in Soil Associated Metagenomes Align Most Closely to those in the Genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia

Propanotrophs are a focus of interest because of their ability to degrade numerous environmental contaminants. To explore the phylogeny of microorganisms containing the propane monooxygenase gene cluster (prmABCD), NCBI bacterial genomes and publicly available soil associated metagenomes (from soils, rhizospheres, tree roots) were both examined. Nucleic acid sequences were collected only if all four subunits were located together, were of the expected length and were annotated as propane monooxygenase subunits. In the bacterial genomes, this resulted in data collection only from the phyla Actinomycetota and Pseudomonadota. For the soil associated metagenomes, reads from four studies were subject to quality control, assembly and annotation. Following this, the propane monooxygenase subunit nucleic acid sequences were collected and aligned to the collected bacterial sequences. In total, forty-two propane monooxygenase gene clusters were annotated from the soil associated metagenomes. The majority aligned closely to those from the Actinomycetota, followed by the Alphaproteobacteria, then the Betaproteobacteria. Actinomycetota aligning propane monooxygenase sequences were obtained from all four datasets and most closely aligned to the genera Kribbella and Amycolatopsis. Alphaproteobacteria aligning sequences largely originated from metagenomes associated with miscanthus and switchgrass rhizospheres and primarily aligned with the genera Bradyrhizobium, Acidiphilium and unclassified Rhizobiales. Betaproteobacteria aligning sequences were obtained from only the Red Oak root metagenomes and primarily aligned with the genera Paraburkholderia, Burkholderia and Caballeronia. Interestingly, sequences from the environmental metagenomes were not closely aligned to those from well-studied propanotrophs, such as Mycobacterium and Rhodococcus. Overall, the study highlights the previously unreported diversity of putative propanotrophs in environmental samples. The common occurrence of propane monooxygenase gene clusters has implications for their potential use for contaminant biodegradation.

A multicomponent propane monooxygenase catalyzes the initial degradation of methyl tert-butyl ether in Mycobacterium vaccae JOB5

Methyl tert-butyl ether (MTBE) has been recognized as a groundwater contaminant due to its widespread distribution and potential threat to human health. The limited understanding of the enzymes catalyzing MTBE degradation restricts their application in MTBE bioremediation. In this study, an MTBE-degrading soluble di-iron monooxygenase that clusters phylogenetically with a known propane monooxygenase (PRM) encoded by the prmABCD gene cluster was identified and functionally characterized, revealing their role in MTBE metabolism by Mycobacterium vaccae JOB5. Transcriptome analysis demonstrated that the expression of prmABCD was upregulated when JOB5 was induced by MTBE. Escherichia coli Rosetta heterologously expressing prmABCD from JOB5 could transform MTBE, indicating that the PRM of JOB5 is capable of the initial degradation of MTBE. The loss of the gene encoding the oxygenase α-subunit or β-subunit, the coupling protein, or the reductase disrupted MTBE transformation by the recombinant E. coli Rosetta. In addition, the catalytic capacity of PRM is likely affected by residue G95 in the active site pocket and residues I84, P165, A269, and V270 in the substrate tunnel structure. Mutation of amino acids in the active site and substrate tunnel resulted in inefficiency or inactivation of MTBE degradation, and the activity in 1,4-dioxane (1,4-D) degradation was diminished less than that in MTBE degradation.IMPORTANCEMulticomponent monooxygenases catalyzing the initial hydroxylation of MTBE are important in MTBE biodegradation. Previous studies of MTBE degradation enzymes have focused on P450s, alkane monooxygenase and MTBE monooxygenase, but the vital role of soluble di-iron monooxygenases has rarely been reported. In this study, we deciphered the essential catalytic role of a PRM and revealed the key residues of the PRM in MTBE metabolism. Our findings provide new insight into the MTBE-degrading gene cluster and enzymes in bacteria. This characterization of the PRM associated with MTBE degradation expands our understanding of MTBE-degrading gene diversity and provides a novel candidate enzyme for the bioremediation of MTBE-contaminated sites.

Bioreduction of Cr(VI) using a propane-based membrane biofilm reactor

The strong physiological toxicity of Cr(VI) makes it widely concerned in wastewater treatment. At present, the simplest and harmless method for treating Cr(VI) is known to be biologically reducing it to Cr(III), making it precipitate as Cr(OH)₃(s), and then removing Cr(III) by solid separation technology. Studies have shown that Cr(VI) reduction bacteria can use CH₄ and H₂ as electron donors to reduce Cr(VI). Based on this, in this study, C₃H₈ was used as the only electron donor to investigate the potential of C₃H₈ matrix membrane bioreactor in the Cr(VI) wastewater treatment. The experiment was divided into three stages, each of which run stably for at least 30 days, and the whole process run for 120 days in total. The experiment is divided into three stages, each stage runs stably for at least 30 days, for a total of 120 days. With the increase of the Cr(VI) load, the removal rate gradually decreased. In stage 3, when Cr(VI) concentration was 2.0 mg·L^-1, the removal rate was reduced from 90% in the first stage to 75%. According to X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis, it is known that Cr(III) is the main product during this process and it is adsorbed on the biofilm as Cr(OH)₃ precipitate. During the experiment, the amount of extracellular polymeric substance (EPS) produced by microorganisms increased initially and then decreased, and the amount of polysaccharides (PS) was always more than protein (PN). By analyzing the microbial community structure after inoculating sludge and adding Cr(VI), Nocardia and Rhodococcus dominate the biofilm samples. Chromate reductase, cytochrome c, nitrate reductase, and other functional genes related to chromate reductase increased gradually during the experiment.

The association of air pollutants (CO2, MTBE) on Candida albicans and Candida glabrata drug resistance

Introduction

Therapeutic methods are very important in the prevalence of opportunistic fungal infections, which are an important cause of human diseases. In this study, air pollution agents that are in direct contact with microorganisms, and the effects of carbon sources using CO2 and MTBE on growth of fungi, and particularly the evaluation of changes in the expression of interfering genes in susceptibility and drug resistance in these fungi, were investigated.

Materials and Methods

Collecting samples and isolating Candida glabrata and Candida albicans with phenotypic methods were accomplished. We then evaluated the minimum inhibitory concentration (MIC) with the M27A4 protocol of CLSI. We adjusted 20 strains of C. albicans and 10 strains of C. glabrata whose sensitivity was evaluated in the MIC test with 5% CO2 and 5mg/ml methyl tert-butyl ether (MTBE) considered as air pollutants, and followed by re-evaluating MIC testing to separate azole-resistant strains. Interfering agents were also considered.

Results

Upregulation of some genes on the two mentioned yeasts had led to drug resistance in them; they were previously sensitive to both drugs. Correspondingly, 41% of C. glabrata samples in sputum showed sensitivity to these drugs. Upregulation of ERG11 (71%) and EPA1 (90%) were observed in resistant strains. Upregulation of genes associated with aspartate proteins and downregulation of SAP3 genes were recognized in C. glabrata in sputum and a 15% downregulation of bronchoalveolar lavage (BAL) isolate and 50% upregulation of SAP1 gene in C. albicans sensitive samples were observed and compared to fluconazole and itraconazole with the oral and joint sources. Remarkably, decreased SAP2 expression in oral sources and a 60% increase in resistant strains in C. albicans were observed. The downregulation of SAP3 expression showed in the joint samples. An increase in HWP1 expression (30%) was noted in isolated and drug-sensitive samples at the sputum and BAL source. CDR1 expression was increased in MTBE-affected species; however, it decreased in the vicinity of CT.

Conclusions

Air pollutants such as CO2 and MTBE eventually caused drug resistance in Candida, which can be one of the causes of drug resistance in candidiasis infections.

Distinct Catalytic Behaviors between Two 1,4-Dioxane-Degrading Monooxygenases: Kinetics, Inhibition, and Substrate Range

Monitored natural attenuation (MNA) and engineered bioremediation have been recognized as effective and cost-efficient in situ treatments to mitigate 1,4-dioxane (dioxane) contamination. Dioxane metabolism can be initiated by two catabolic enzymes, propane monooxygenase (PRM) and tetrahydrofuran monooxygenase (THM), belonging to the group-6 and 5 of soluble di-iron monooxygenase family, respectively. In this study, we comprehensively compared catalytic behaviors of PRM and THM when individually expressed in the heterologous host, Mycobacterium smegmatis mc²-155. Kinetic results revealed a half-saturation coefficient (K_m) of 53.0 ± 13.1 mg/L for PRM, nearly 4 times lower than that of THM (235.8 ± 61.6 mg/L), suggesting that PRM has a higher affinity to dioxane. Exposure with three common co-contaminants (1,1-dichloroethene, trichloroethene, and 1,1,1-trichloroethane) demonstrated that PRM was also more resistant to their inhibition than THM. Thus, dioxane degraders expressing PRM may be more physiologically and ecologically advantageous than those with THM at impacted sites, where dioxane concentration is relatively low (e.g., 250 to 1000 μg/L) with co-occurrence of chlorinated solvents (e.g., 0.5 to 8 mg/L), underscoring the need of surveying both PRM and THM-encoding genes for MNA potential assessment. PRM is also highly versatile, which breaks down cyclic molecules (dioxane, tetrahydrofuran, and cyclohexane), as well as chlorinated and aromatic pollutants, including vinyl chloride, 1,2-dichloroethane, benzene, and toluene. This is the first report regarding the ability of PRM to degrade a variety of short-chain alkanes and ethene in addition to dioxane, unraveling its pivotal role in aerobic biostimulation that utilizes propane, isobutane, or other gaseous alkanes/alkenes (e.g., ethane, butane, and ethene) to select and fuel indigenous microorganisms to tackle the commingled contamination of dioxane and chlorinated compounds.